Noble Six discovers the data pad containing the "latch key" at the Sorvad Relay Outpost. Kat decodes the data on Noble Team's way to Sword Base which, in turn, helps Dr. Halsey unlock the secrets to the Forerunner structure near the end of the game. However, no one tells us what these secrets were. It couldn't have been the location of Halo, because the crew of the Pillar of Autumn had no idea what Halo was when they first discovered it. If Cortana somehow contained the secrets unlocked from the Forerunner structure beneath Sword Base, then why didn't she tell anybody? It couldn't have been the time-space-warping crystal from the novel Halo: First Strike, because Dr. Halsey didn't know of its existence until she discovered it beneath Castle Base.
It doesn't make sense, because none of that comes to light in the Halo Trilogy nor the books. Maybe it'll be revealed in Halo 4 or Halo: Anniversary, though I very much doubt it.
Also, how did the Covenant supercarrier, Long Night of Solace, make foothold on Reach without anyone batting an eye? It's a huge mass. I'm pretty sure the Remote Sensor Outposts in the region would've picked up something that large on their sensors in slip-space. It couldn't have been cloaked, because the Spires were needed to cloak the ship. So how did that ship bypass Reach's defenses?
And why didn't the Orbital Mac Guns rain hell down on Long Night of Solace? The UNSC had twenty of them. Once it revealed itself after the destruction of the Spire, Reach's orbital defenses could've made quick work of its shields and hull.
If they destroyed Long Night of Solace on the spot when it was revealed after the destruction of the Spire, then Jorge wouldn't have died so early on in the game. In fact, he probably would've survived 'till the end. He would've hopped onto the Mass Driver and let Noble Six escape with Captain Keyes. Then Noble Six would've gone to Halo with John-117 and they would've kicked so much ass that the universe would collapse on itself; it couldn't take the awesomeness.
Also, where the hell was the UNSC fleet orbiting Reach? The UNSC had a total of 1,209 Naval assets on site at all times (I know I'm right, because I looked it up on this site). And throughout the entire game we saw only, like, what... about five frigates? Long Night of Solace couldn't have wiped out the ENTIRE Eridani Fleet out, because the rest of the Covenant fleet hadn't arrived yet and that would mean that the UNSC are completely worthless and humanity would've been extinct for about 20 years by now. And seeing how humanity won the war at the end of Halo 3, with the help of the Elites, that proves the UNSC wasn't completely useless. So where the hell was the UNSC Eridani Fleet at Reach?
Ugh. Maybe I've been looking too much into this. Anyway, those are my thoughts on the matter. There's no need for any of you to reply. This is just something for you all to ponder. Exorcise that noggin.
If you read through all this, then that means you had nothing better to do with your time today, too! Virtual high-five time, buddy! Yeah!